EDA

Overall

Demographic and Clinical Characteristics
Variable Category Value
Age at Diagnosis - 30.7 ± 13.1 (0-80)
Sex Male 178 (11.3%)
Female 1402 (88.6%)
Race White 933 (59.0%)
Black 233 (14.7%)
Chinese 153 (9.7%)
Other 101 (6.4%)
Native North American 13 (0.8%)
Filipino 70 (4.4%)
Mixed 30 (1.9%)
Vital Status Active 1043 (65.9%)
Dead 198 (12.5%)
Lost to Follow-up 5 (0.3%)
Green Chart 314 (19.8%)
Discharged from Clinic 1 (0.1%)
No Consent 3 (0.2%)
Questionnaire 17 (1.1%)
Employment Status disabled 317 (20.0%)
sick leave 57 (3.6%)
homemaker 165 (10.4%)
retired 163 (10.3%)
looking for work 45 (2.8%)
employed 835 (52.8%)
Number of Visits - 22.0 ± 28.4 (1-179)

By Employment Status

Employment Status Characteristics (Sorted by Count)
Employment Status
Category Variable Employed Disability Benefit Economically Inactive Student Retired Unemployed
Counts N 886 217 188 161 78 52
% of Cohort 886 (56.0%) 217 (13.7%) 188 (11.9%) 161 (10.2%) 78 (4.9%) 52 (3.3%)
Sex % Male 105 (11.9%) 22 (10.1%) 2 (1.1%) 24 (14.9%) 20 (25.6%) 5 (9.6%)
% Female 780 (88.1%) 195 (89.9%) 185 (98.9%) 137 (85.1%) 58 (74.4%) 47 (90.4%)
Age (Diagnosis) Mean Age (At Diagnosis) 30.4 32.8 34.4 17.1 50.5 26.3
SD Age (At Diagnosis) 11.4 11.5 13.6 5.4 15.9 8.9
Median Age (At Diagnosis) 29 33 32 16 52 24.5
Age (1st Visit) Mean Age (1st Visit) 38.1 43.8 45.5 21.5 65.3 32.5
SD Age (1st Visit) 11.1 10.8 13.6 4.8 9.2 8.4
Median Age (1st Visit) 36.9 43.7 43.4 19.8 65.9 31
Race % White 514 (60.5%) 129 (61.1%) 129 (70.5%) 77 (47.8%) 59 (75.6%) 25 (49.0%)
% Black 135 (15.9%) 43 (20.4%) 16 (8.7%) 21 (13.0%) 8 (10.3%) 10 (19.6%)
% Chinese 79 (9.3%) 13 (6.2%) 13 (7.1%) 34 (21.1%) 8 (10.3%) 6 (11.8%)
% Other 54 (6.4%) 9 (4.3%) 17 (9.3%) 15 (9.3%) 2 (2.6%) 4 (7.8%)
% Native 5 (0.6%) 6 (2.8%) 2 (1.1%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
% Filipino 45 (5.3%) 9 (4.3%) 3 (1.6%) 7 (4.3%) 1 (1.3%) 5 (9.8%)
% Mixed 17 (2.0%) 2 (1.0%) 3 (1.6%) 7 (4.3%) 0 (0.0%) 1 (2.0%)
Status % Active 645 (72.9%) 111 (51.1%) 103 (54.8%) 127 (78.9%) 22 (28.2%) 35 (67.3%)
% Dead 70 (7.9%) 48 (22.1%) 36 (19.2%) 10 (6.2%) 30 (38.5%) 4 (7.7%)
% Lost 4 (0.4%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (1.9%)
% Green Chart 155 (17.5%) 53 (24.4%) 47 (25.0%) 23 (14.3%) 24 (30.8%) 12 (23.1%)
% Discharged 0 (0.0%) 0 (0.0%) 0 (0.0%) 1 (0.6%) 0 (0.0%) 0 (0.0%)
% No Consent 3 (0.3%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
% Questionnaire 8 (0.9%) 5 (2.3%) 2 (1.1%) 0 (0.0%) 2 (2.6%) 0 (0.0%)
% Questionnaire2 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%) 0 (0.0%)
Vertical Summary by Initial Employment Status
Metric Disability Benefit Economically Inactive Employed Retired Student Unemployed
N 217 188 886 78 161 52
Median Visits 17 20.5 17.5 16.5 23 11
Visit Range 1 - 91 1 - 93 1 - 94 1 - 68 3 - 85 1 - 62
IQR Visits 6 - 38 7 - 39 8 - 36 4 - 28.5 16 - 34 5 - 26.75
Median Obs (months) 100.804862023653 122.174770039422 112.023653088042 101.182654402102 142.509855453351 63.7647831800263
Median Time Between Visits (months) 3.90932982917214 3.90932982917214 3.94218134034166 4.13929040735874 4.13929040735874 3.90932982917214
Median Transitions 0 0 0 0 1 1
Transition Range 0 - 4 0 - 11 0 - 9 0 - 2 1 - 8 0 - 5
Initial SLEDAI 6 4 4 2 4 5
Final SLEDAI 2 2 2 2 2 2
Mean SLEDAI 4 2.88888888888889 3.22144522144522 2.11213517665131 4 3.84962406015038

Vertical Summary by Initial Employment Status
Metric disabled employed homemaker looking for work retired sick leave student
N 217 796 188 52 78 90 161
Median Visits 17 17 20.5 11 16.5 22 23
Visit Range 1 - 91 1 - 94 1 - 93 1 - 62 1 - 68 2 - 74 3 - 85
IQR Visits 6 - 38 7 - 35.25 7 - 39 5 - 26.75 4 - 28.5 13.25 - 39 16 - 34
Median Obs (months) 100.804862023653 109.691195795007 122.174770039422 63.7647831800263 101.182654402102 132.178055190539 142.509855453351
Median Time Between Visits (months) 3.90932982917214 4.02431011826544 3.90932982917214 3.90932982917214 4.13929040735874 3.76971090670171 4.13929040735874
Median Transitions 0 0 0 1 0 1 1
Transition Range 0 - 4 0 - 9 0 - 11 0 - 6 0 - 2 0 - 7 1 - 8
Initial SLEDAI 6 4 4 5 2 8 4
Final SLEDAI 2 2 2 2 2 2 2
Mean SLEDAI 4 3.2 2.88888888888889 3.84962406015038 2.11213517665131 3.44155844155844 4
Ever Retired 12 (5.5%) 61 (7.7%) 12 (6.4%) 0 (0%) 78 (100%) 7 (7.8%) 1 (0.6%)
Ever Disabled 217 (100%) 103 (12.9%) 15 (8%) 6 (11.5%) 1 (1.3%) 37 (41.1%) 21 (13%)
Ever Homemaker 6 (2.8%) 33 (4.1%) 188 (100%) 0 (0%) 2 (2.6%) 14 (15.6%) 7 (4.3%)
Ever Student 2 (0.9%) 16 (2%) 6 (3.2%) 5 (9.6%) 0 (0%) 6 (6.7%) 161 (100%)
Ever Looking 4 (1.8%) 37 (4.6%) 9 (4.8%) 52 (100%) 0 (0%) 5 (5.6%) 18 (11.2%)
Ever Employed 22 (10.1%) 796 (100%) 35 (18.6%) 29 (55.8%) 1 (1.3%) 31 (34.4%) 143 (88.8%)
Ever Sick Leave 3 (1.4%) 63 (7.9%) 3 (1.6%) 3 (5.8%) 1 (1.3%) 90 (100%) 15 (9.3%)
Final Retired 11 (5.1%) 58 (7.3%) 12 (6.4%) 0 (0%) 75 (96.2%) 7 (7.8%) 0 (0%)
Final Disabled 181 (83.4%) 78 (9.8%) 11 (5.9%) 4 (7.7%) 1 (1.3%) 28 (31.1%) 14 (8.7%)
Final Homemaker 4 (1.8%) 19 (2.4%) 131 (69.7%) 0 (0%) 1 (1.3%) 7 (7.8%) 3 (1.9%)
Final Student 0 (0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%) 0 (0%)
Final Looking 1 (0.5%) 11 (1.4%) 3 (1.6%) 22 (42.3%) 0 (0%) 1 (1.1%) 7 (4.3%)
Final Employed 18 (8.3%) 609 (76.5%) 30 (16%) 26 (50%) 0 (0%) 22 (24.4%) 130 (80.7%)
Final Sick Leave 2 (0.9%) 21 (2.6%) 1 (0.5%) 0 (0%) 1 (1.3%) 25 (27.8%) 7 (4.3%)
Changed Status 43 (19.8%) 242 (30.4%) 62 (33%) 32 (61.5%) 5 (6.4%) 68 (75.6%) 161 (100%)
Proportion of Patients by Initial Employment State with Exactly N Transitions
Number of Transitions
Initial Employment Category 0 1 2 3 4 5 7 11 6 8 9
Employed 64.2% 21.6% 7.4% 3.6% 2.1% 0.5% 0.1% 0.0% 0.2% 0.1% 0.1%
Student 0.0% 73.3% 11.2% 8.7% 1.9% 1.9% 1.2% 0.0% 1.2% 0.6% 0.0%
Disability Benefit 80.2% 12.9% 3.7% 2.3% 0.9% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
Economically Inactive 67.6% 22.9% 3.2% 3.7% 1.1% 0.5% 0.5% 0.5% 0.0% 0.0% 0.0%
Retired 93.6% 2.6% 3.8% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
Unemployed 38.5% 42.3% 13.5% 0.0% 1.9% 3.8% 0.0% 0.0% 0.0% 0.0% 0.0%

Most Common Transitions From Each Status
Origin Age Group Most Common Next Category Proportion Total Transitions
Disability Benefit 20-29 Employed 66.7% 21
Disability Benefit 30-39 Employed 81.0% 42
Disability Benefit 40-49 Employed 67.7% 31
Disability Benefit 50-59 Employed 53.8% 26
Disability Benefit 60-69 Retired 72.7% 22
Disability Benefit 70+ Retired 100.0% 5
Disability Benefit <20 Student 100.0% 1
Economically Inactive 20-29 Employed 37.5% 8
Economically Inactive 30-39 Employed 66.7% 36
Economically Inactive 40-49 Employed 60.6% 33
Economically Inactive 50-59 Disability Benefit 42.9% 14
Economically Inactive 60-69 Retired 66.7% 9
Economically Inactive 70+ Retired 85.7% 7
Employed 20-29 Disability Benefit 47.6% 84
Employed 30-39 Disability Benefit 61.4% 114
Employed 40-49 Disability Benefit 60.6% 94
Employed 50-59 Disability Benefit 57.8% 90
Employed 60-69 Disability Benefit 45.5% 44
Employed 70+ Retired 100.0% 9
Employed <20 Student 66.7% 12
Retired 30-39 Employed 100.0% 2
Retired 40-49 Employed 100.0% 1
Retired 50-59 Disability Benefit 33.3% 3
Retired 60-69 Employed 62.5% 8
Retired 70+ Disability Benefit 50.0% 4
Student 20-29 Employed 80.5% 159
Student 30-39 Employed 72.7% 33
Student 40-49 Employed 50.0% 10
Student 50-59 Employed 100.0% 1
Student <20 Employed 94.7% 19
Unemployed 20-29 Employed 79.4% 34
Unemployed 30-39 Employed 69.6% 23
Unemployed 40-49 Employed 72.0% 25
Unemployed 50-59 Employed 70.0% 10
Unemployed 60-69 Employed 66.7% 3
Unemployed <20 Employed 66.7% 3

Disease Activity

Slicc Damage Index

Original Employment Categories

New Employment States

Dead vs Alive

Overall

## # A tibble: 12 × 7
##    GROUP             visit_type n_patients mean_SLEDAI se_SLEDAI mean_SDI se_SDI
##    <fct>             <fct>           <int>       <dbl>     <dbl>    <dbl>  <dbl>
##  1 Alive (Active/Gr… Final            1326        2.80    0.0939    1.59  0.0548
##  2 Alive (Active/Gr… Initial          1357        6.69    0.178     0.498 0.0288
##  3 Alive (Active/Gr… Middle           1226        3.56    0.111     1.12  0.0451
##  4 Dead – Lupus      Final               9        4       1.20      4.33  0.866 
##  5 Dead – Lupus      Initial             9        5.22    0.572     2.33  0.601 
##  6 Dead – Lupus      Middle              9        3.89    0.790     3.11  0.588 
##  7 Dead – Lupus (Se… Final              18        6.61    1.36      3     0.417 
##  8 Dead – Lupus (Se… Initial            19        6.95    1.11      0.944 0.310 
##  9 Dead – Lupus (Se… Middle             17        5.59    1.26      1.82  0.472 
## 10 Dead – Other      Final             159        4.63    0.442     3.81  0.213 
## 11 Dead – Other      Initial           170        6.32    0.510     1.86  0.174 
## 12 Dead – Other      Middle            151        4.31    0.369     2.73  0.202

SLEDAI

SDI

Site Specific

## # weights:  90 (70 variable)
## initial  value 2578.341876 
## iter  10 value 1633.612618
## iter  20 value 1541.555838
## iter  30 value 1524.802597
## iter  40 value 1518.945487
## iter  50 value 1516.987064
## iter  60 value 1516.284369
## iter  70 value 1515.960374
## iter  80 value 1515.908963
## final  value 1515.908401 
## converged

## # weights:  84 (65 variable)
## initial  value 1743.381964 
## iter  10 value 1239.842205
## iter  20 value 1110.841505
## iter  30 value 1088.199776
## iter  40 value 1085.194522
## iter  50 value 1084.925333
## iter  60 value 1084.839796
## iter  70 value 1084.836621
## final  value 1084.836582 
## converged
## # weights:  84 (65 variable)
## initial  value 1743.381964 
## iter  10 value 1239.842205
## iter  20 value 1110.841505
## iter  30 value 1088.199776
## iter  40 value 1085.194522
## iter  50 value 1084.925333
## iter  60 value 1084.839796
## iter  70 value 1084.836621
## final  value 1084.836582 
## converged
## # weights:  90 (70 variable)
## initial  value 2578.341876 
## iter  10 value 1633.612618
## iter  20 value 1541.555838
## iter  30 value 1524.802597
## iter  40 value 1518.945487
## iter  50 value 1516.987064
## iter  60 value 1516.284369
## iter  70 value 1515.960374
## iter  80 value 1515.908963
## final  value 1515.908401 
## converged

Analysis

Markov Transition Matrix

## [1] "Transition Counts:"
##                        to_cat
## from_cat                Disability Benefit Economically Inactive Employed
##   Disability Benefit                  8422                    18       86
##   Economically Inactive                 24                  4551       56
##   Employed                             240                    53    17403
##   Retired                                6                     3        9
##   Student                               21                     4      176
##   Unemployed                            11                     7       72
##                        to_cat
## from_cat                Retired Student Unemployed
##   Disability Benefit         28      11          5
##   Economically Inactive      14       5          9
##   Employed                   59      39         56
##   Retired                  2941       0          0
##   Student                     0    1594         21
##   Unemployed                  2       6        745
## [1] "\nTransition Probability Matrix:"
##                        to_cat
## from_cat                Disability Benefit Economically Inactive Employed
##   Disability Benefit                 0.983                 0.002    0.010
##   Economically Inactive              0.005                 0.977    0.012
##   Employed                           0.013                 0.003    0.975
##   Retired                            0.002                 0.001    0.003
##   Student                            0.012                 0.002    0.097
##   Unemployed                         0.013                 0.008    0.085
##                        to_cat
## from_cat                Retired Student Unemployed
##   Disability Benefit      0.003   0.001      0.001
##   Economically Inactive   0.003   0.001      0.002
##   Employed                0.003   0.002      0.003
##   Retired                 0.994   0.000      0.000
##   Student                 0.000   0.878      0.012
##   Unemployed              0.002   0.007      0.884

Markov Transition Probability Matrix
To State
From To: Disability Benefit To: Economically Inactive To: Employed To: Retired To: Student To: Unemployed
Disability Benefit 98.3% 0.2% 1.0% 0.3% 0.1% 0.1%
Economically Inactive 0.5% 97.7% 1.2% 0.3% 0.1% 0.2%
Employed 1.3% 0.3% 97.5% 0.3% 0.2% 0.3%
Retired 0.2% 0.1% 0.3% 99.4%
Student 1.2% 0.2% 9.7%
87.8% 1.2%
Unemployed 1.3% 0.8% 8.5% 0.2% 0.7% 88.4%
Note:
Probabilities represent the likelihood of transitioning from row states to column states.
‘-’ indicates zero probability transitions. 
## [1] "Transition Counts:"
##                        to_cat
## from_cat                Disability Benefit Economically Inactive Employed
##   Disability Benefit                  8422                    18       86
##   Economically Inactive                 24                  4551       55
##   Employed                             240                    53    17401
##   Retired                                6                     3        9
##   Student                               21                     4      176
##   Unemployed                            11                     7       72
##                        to_cat
## from_cat                Retired Student Unemployed
##   Disability Benefit         28      11          5
##   Economically Inactive      14       5          9
##   Employed                   59      39         56
##   Retired                  2941       0          0
##   Student                     0    1594         21
##   Unemployed                  2       6        745
## [1] "\nTransition Probability Matrix:"
##                        to_cat
## from_cat                Disability Benefit Economically Inactive Employed
##   Disability Benefit                 0.983                 0.002    0.010
##   Economically Inactive              0.005                 0.977    0.012
##   Employed                           0.013                 0.003    0.975
##   Retired                            0.002                 0.001    0.003
##   Student                            0.012                 0.002    0.097
##   Unemployed                         0.013                 0.008    0.085
##                        to_cat
## from_cat                Retired Student Unemployed
##   Disability Benefit      0.003   0.001      0.001
##   Economically Inactive   0.003   0.001      0.002
##   Employed                0.003   0.002      0.003
##   Retired                 0.994   0.000      0.000
##   Student                 0.000   0.878      0.012
##   Unemployed              0.002   0.007      0.884

Proposed Analysis

Competing Risk Analysis

Markov model

##                        to_cat
## from_cat                Disability Benefit Economically Inactive Employed
##   Disability Benefit                  8422                    18       86
##   Economically Inactive                 24                  4551       55
##   Employed                             240                    53    17401
##   Retired                                6                     3        9
##   Student                               21                     4      176
##   Unemployed                            11                     7       72
##                        to_cat
## from_cat                Retired Student Unemployed
##   Disability Benefit         28      11          5
##   Economically Inactive      14       5          9
##   Employed                   59      39         56
##   Retired                  2941       0          0
##   Student                     0    1594         21
##   Unemployed                  2       6        745

Trajectories

## # A tibble: 10 × 3
##    simplified_trajectory                        n   prop
##    <chr>                                    <int>  <dbl>
##  1 Employed → Disability Benefit              130 0.202 
##  2 Student → Employed                         112 0.174 
##  3 Employed → Retired                          45 0.0698
##  4 Employed → NA                               25 0.0388
##  5 Employed → Disability Benefit → Employed    22 0.0341
##  6 Employed → Economically Inactive            21 0.0326
##  7 Economically Inactive → Employed            19 0.0295
##  8 Unemployed → Employed                       19 0.0295
##  9 Disability Benefit → Employed               15 0.0233
## 10 Employed → Disability Benefit → Retired     13 0.0202

## 
## Data validation:
## Unique initial EMPs: disabled, homemaker, employed, retired, sick leave, student, looking for work
## Time range (years): 0 28.13415
## Number of transitions to 'disabled': 0
## quartz_off_screen 
##                 2
Kaplan Meier Plot
Kaplan Meier Plot
## 
##    Low score_n Medium score_n   High score_n 
##           1521              0              0

## Call:
## coxph(formula = Surv(time, event) ~ SLEDAI2_I, data = surv_data)
## 
##   n= 1521, number of events= 193 
## 
##                coef exp(coef)  se(coef)      z Pr(>|z|)
## SLEDAI2_I -0.005754  0.994262  0.011208 -0.513    0.608
## 
##           exp(coef) exp(-coef) lower .95 upper .95
## SLEDAI2_I    0.9943      1.006    0.9727     1.016
## 
## Concordance= 0.503  (se = 0.023 )
## Likelihood ratio test= 0.27  on 1 df,   p=0.6
## Wald test            = 0.26  on 1 df,   p=0.6
## Score (logrank) test = 0.26  on 1 df,   p=0.6
## Call:
## coxph(formula = Surv(time, event) ~ score_n, data = surv_data)
## 
##   n= 1521, number of events= 193 
## 
##            coef exp(coef) se(coef)     z Pr(>|z|)    
## score_n 0.37712   1.45808  0.03112 12.12   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##         exp(coef) exp(-coef) lower .95 upper .95
## score_n     1.458     0.6858     1.372      1.55
## 
## Concordance= 0.693  (se = 0.022 )
## Likelihood ratio test= 101.3  on 1 df,   p=<2e-16
## Wald test            = 146.8  on 1 df,   p=<2e-16
## Score (logrank) test = 166.6  on 1 df,   p=<2e-16
## Call:
## coxph(formula = Surv(time, event) ~ SLEDAI2_I + score_n + AGE_DX + 
##     SEX, data = surv_data)
## 
##   n= 1520, number of events= 193 
##    (1 observation deleted due to missingness)
## 
##                coef exp(coef)  se(coef)      z Pr(>|z|)    
## SLEDAI2_I  0.012295  1.012371  0.011363  1.082   0.2793    
## score_n    0.395148  1.484604  0.032195 12.273   <2e-16 ***
## AGE_DX     0.045519  1.046571  0.005149  8.840   <2e-16 ***
## SEXFemale -0.419165  0.657596  0.194700 -2.153   0.0313 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##           exp(coef) exp(-coef) lower .95 upper .95
## SLEDAI2_I    1.0124     0.9878    0.9901    1.0352
## score_n      1.4846     0.6736    1.3938    1.5813
## AGE_DX       1.0466     0.9555    1.0361    1.0572
## SEXFemale    0.6576     1.5207    0.4490    0.9631
## 
## Concordance= 0.763  (se = 0.02 )
## Likelihood ratio test= 178.9  on 4 df,   p=<2e-16
## Wald test            = 226.4  on 4 df,   p=<2e-16
## Score (logrank) test = 254  on 4 df,   p=<2e-16

Death vs Alive

## 
##  Welch Two Sample t-test
## 
## data:  SLEDAI2_I by status_group
## t = -9.6156, df = 5911.1, p-value < 2.2e-16
## alternative hypothesis: true difference in means between group Alive and group Deceased is not equal to 0
## 95 percent confidence interval:
##  -0.7855660 -0.5194987
## sample estimates:
##    mean in group Alive mean in group Deceased 
##               3.412106               4.064638
## 
##  Welch Two Sample t-test
## 
## data:  score_n by status_group
## t = -37.685, df = 5467, p-value < 2.2e-16
## alternative hypothesis: true difference in means between group Alive and group Deceased is not equal to 0
## 95 percent confidence interval:
##  -1.509364 -1.360092
## sample estimates:
##    mean in group Alive mean in group Deceased 
##               1.450114               2.884842

Trajectories

## Creating Sankey diagram for initial category: Economically Inactive 
## Creating Sankey diagram for initial category: Employed 
## Creating Sankey diagram for initial category: Disability Benefit 
## Creating Sankey diagram for initial category: Student 
## Creating Sankey diagram for initial category: Unemployed 
## Creating Sankey diagram for initial category: Retired

Employed

Economically Inactive

Disability Benefit

Student

Retired

Unemployed